Method for analyzing biological elements

1. A method for analyzing biological elements, comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said first set of biological elements represent genes with increased RNA transcription and said second set of biological elements are genes.

2. The method as in claim 1 , wherein said genes with increased RNA transcription are selected based on a single RNA transcription profiling.

3. A method for analyzing biological elements, comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said first set and said second set comprise elements that are not all of a single type.

4. A method for analyzing biological elements, comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said algorithm is selected from the group consisting of the shortest path heuristic, the minimum spanning tree heuristic, the distance network heuristic, and the simulated annealing heuristic.

5. A method for analyzing biological elements, comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said algorithm comprises a minimum spanning tree heuristic.

6. A method for analyzing biological elements, comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements; and, d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraphs with more edges than said first Steiner subgraph.

7. A method for analyzing biological elements, comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said edges in said graph are differentially weighted.

8. The method as in claim 7 , wherein said edges are differentially weighted according to known biorelationships.

9. The method of claim 7 , wherein said algorithm creates a Steiner subgraph with the lowest possible total edge weight said algorithm can determine, and further comprising d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraphs with having edges of greater total edge weight than said first Steiner subgraph.

10. A method for analyzing genes, comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said first set of genes represent genes with increased RNA transcription.

11. The method as in claim 10 , wherein said genes with increased RNA transcription are selected based on a single RNA transcription profiling.

12. A method for analyzing genes, comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said algorithm is selected from the group consisting of the shortest path heuristic, the minimum spanning tree heuristic, the distance network heuristic, and the simulated annealing heuristic.

13. A method for analyzing genes, comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said algorithm comprises a minimum spanning tree heuristic.

14. A method for analyzing genes, comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes; and, d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraphs with more edges than said first Steiner subgraph.

15. A method for analyzing genes, comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said edges in said graph are differentially weighted.

16. The method as in claim 15 , wherein said edges are differentially weighted according to known biorelationships.

17. The method of claim 15 , wherein said algorithm creates a Steiner subgraph with the lowest possible total edge weight said algorithm can determine, and further comprising d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraphs having edges of greater total edge weight than said first Steiner subgraph.

18. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze biological elements, said method steps comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said first set of biological elements represent genes with increased RNA transcription and said second set of biological elements are genes.

19. The device as in claim 18 , wherein said genes with increased RNA transcription are selected based on a single RNA transcription profiling.

20. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze biological elements, said method steps comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said first set and said second set comprise elements that are not all of a single type.

21. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze biological elements, said method steps comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said algorithm is selected from the group consisting of the shortest path heuristic, the minimum spanning tree heuristic, the distance network heuristic, and the simulated annealing heuristic.

22. A. program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze biological elements, said method steps comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said algorithm comprises a minimum spanning tree heuristic.

23. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze biological elements, said method steps comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements; and, d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraphs with more edges than said first Steiner subgraph.

24. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze biological elements, said method steps comprising: a) providing a first set of biological elements; b) providing a graph representing relationships among a second set of biological elements, wherein said biological elements of said second set of biological elements are represented as vertices of said graph and biorelationships between said biological elements of said second set of biological elements are represented as edges of said graph, and wherein said second set of biological elements comprises said first set of biological elements; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of biological elements and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of biological elements and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of biological elements, wherein said edges in said graph are differentially weighted.

25. The device as in claim 24 , wherein said edges are differentially weighted according to known biorelationships.

26. The device of claim 24 , wherein said algorithm creates a Steiner subgraph with the lowest possible total edge weight said algorithm can determine, and further comprising d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraghs with having edges of greater total edge weight than said first Steiner subgragh.

27. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze genes, said method steps comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said first set of genes represent genes with increased RNA transcription.

28. The device as in claim 27 , wherein said genes with increased RNA transcription are selected based on a single RNA transcription profiling.

29. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze genes, said method steps comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said algorithm is selected from the group consisting of the shortest path heuristic, the minimum spanning tree heuristic, the distance network heuristic, and the simulated annealing heuristic.

30. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze genes, said method steps comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said algorithm comprises a minimum spanning tree heuristic.

31. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze genes, said method steps comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes; and, d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraphs with more edges than said first Steiner subgraph.

32. A program storage device readable by a machine, tangibly embodying a program of instructions executable by a machine to perform method steps to analyze genes, said method steps comprising: a) providing a first set of genes; b) providing a graph representing relationships among a second set of genes, wherein said genes of said second set of genes are represented as vertices of said graph and biorelationships between said genes of said second set of genes are represented as edges of said graph, and wherein said second set of genes comprises said first set of genes; and, c) applying an algorithm capable of generating a Steiner Tree to said first set of genes and said graph to create a Steiner subgraph, wherein said Steiner subgraph comprises vertices from said graph corresponding to said first set of genes and further comprises edges and vertices from said graph connecting said vertices from said graph corresponding to said first set of genes, wherein said edges in said graph are differentially weighted.

33. The device as in claim 32 , wherein said edges are differentially weighted according to known biorelationships.

34. The device of claim 32 , wherein said algorithm creates a Steiner subgraph with the lowest possible total edge weight said algorithm can determine, and further comprising d) repeating steps a) through c), wherein said algorithm creates one or more additional Steiner subgraphs with having edges of greater total edge weight than said first Steiner subgraph.